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- PDB-9kr1: Structural Basis for the Polymer-Protein Binding Mechanism of Pol... -

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Basic information

Entry
Database: PDB / ID: 9kr1
TitleStructural Basis for the Polymer-Protein Binding Mechanism of Polyvinyl Alcohol Esterase
ComponentsSGNH/GDSL hydrolase family protein
KeywordsHYDROLASE / Polyvinyl alcohol / degradation / complex structure / molecular mechanism
Function / homologyACETATE ION
Function and homology information
Biological speciesComamonas sp. NyZ500 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsWu, Y.F. / Xu, X.X. / Yin, C.F. / Wang, L.T. / Zhou, N.Y. / Zhou, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Key R&D Program of China2021YFA0909500 China
CitationJournal: Acs Catalysis / Year: 2025
Title: Structural Basis for the Enzyme-Polymer Binding Mechanism of Poly(vinyl alcohol) Esterase
Authors: Wu, Y. / Xu, X. / Yin, C.F. / Shen, Z. / Wang, L. / Zhou, N.Y. / Zhou, J.
History
DepositionNov 27, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SGNH/GDSL hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8316
Polymers42,5741
Non-polymers2575
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.873, 164.873, 164.873
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein SGNH/GDSL hydrolase family protein


Mass: 42573.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence reference for strain 'Comamonas sp. NyZ500' is not available in UniProt at the time of biocuration. The reference sequence from NCBI (id: WP_202789293.1).
Source: (gene. exp.) Comamonas sp. NyZ500 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.39 Å3/Da / Density % sol: 71.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 0.1 M Citric acid pH 3.5, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.84→82.44 Å / Num. obs: 17743 / % possible obs: 99.9 % / Redundancy: 10 % / CC1/2: 0.998 / Rmerge(I) obs: 0.189 / Net I/σ(I): 11.1
Reflection shellResolution: 2.84→2.99 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2573 / CC1/2: 0.897 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.84→82.44 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 19.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.203 990 5.58 %
Rwork0.172 --
obs0.1739 17736 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.84→82.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2895 0 13 68 2976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.946
X-RAY DIFFRACTIONf_dihedral_angle_d15.3491037
X-RAY DIFFRACTIONf_chiral_restr0.054479
X-RAY DIFFRACTIONf_plane_restr0.005520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.84-2.990.25051240.1972388X-RAY DIFFRACTION100
2.99-3.180.21291190.19042398X-RAY DIFFRACTION100
3.18-3.420.251350.20072364X-RAY DIFFRACTION100
3.42-3.760.20041360.16522365X-RAY DIFFRACTION100
3.77-4.310.19491740.15272366X-RAY DIFFRACTION100
4.31-5.430.18051490.15412393X-RAY DIFFRACTION100
5.44-82.440.18961530.17782472X-RAY DIFFRACTION100

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